Molecular sieve electrophoresis is a powerful method for separating macromolecular solutes both among themselves with high resolution on the basis of molecular size and from solutes of lesser molecular size. The gel media in which these separations take place however require careful preparation and special handling techniques, with problems in reproducibility and stability.
Capillary free zone electrophoresis, on the other hand, is also of interest for certain types of separations, since it permits the use of high voltages which provide the advantage of relatively high speed. The small size of the capillary further permits the separation of extremely small samples in a buffer solution without the use of complex media such as a gel or paper, and with relatively little band broadening. Capillary free zone electrophoresis is particularly useful in the separation of small peptides and proteins. Separation occurs on the basis of the charge/mass ratio, however, and for this reason certain separations are very difficult to achieve by this method, notably those involving high molecular weight polynucleotides and many SDS-treated proteins.
Gel media may be placed in capillaries for molecular sieve separations, but the preparation and use of such gels is particularly problematic, since they undergo physical and chemical changes with each use and thus for practical purposes can only be used once. This is detrimental to the reproducibility of the separations and to the efficiency of the technique. In addition, it raises serious problems for those capillaries which are incorporated into cartridges designed for automated instrumentation.